[Bioperl-l] [Bioperl-microarray] SOFT parsers

Allen Day allenday at ucla.edu
Thu Dec 28 18:21:07 EST 2006


> As for R vs. perl, if you are planning on doing analyses of microarray
> data, I would highly suggest looking again at the R/bioconductor
> project.  It will save you reinventing many wheels, such as getting
> annotation like gene ontology and pathways, doing stats, plotting,
> maintaining MIAME-compliant data structures, converting from multiple
> microarray formats, etc.

I'll second this statement WRT the data analysis.  I'm doing all my
analysis in R, Perl is just not good at dealing with large matrices or
plotting.  OTOH, I have also found that R is particularly weak when it
comes to pipelining data and system interfacing.  If your goal is to
do ETL to a local database you're better off using Perl.

I've found they're both about equally clunky for dealing with the
experimental metadata, with a slight preference for Perl.  That's more
a reflection of the baroque MAGE model though than the programming
languages themselves.

-Allen

>
> Sean
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